ArticleBMC genomics2006
Periodicity of SNP distribution around transcription start sites.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Genome-wide annotation of human multi-nucleotide variants reveals widespread functional differences from single nucleotide variants.Nature communications · 2026Article
- Do Genomic Patterns and Fibonacci-Like Regularity Hold the Key to Reproductive Fitness in Livestock?Biochemical genetics · 2026Article
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- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- Altered primary chromatin structures and their implications in cancer development.Cellular oncology (Dordrecht, Netherlands) · 2016Review
- Facilitation of base excision repair by chromatin remodeling.DNA repair · 2015Review
- A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.Open biology · 2015Article
- Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data.International journal of genomics · 2015Article
- Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms.BMC molecular biology · 2014Article
- Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites.PloS one · 2014Article
- The transcript-centric mutations in human genomes.Genomics, proteomics & bioinformatics · 2012Article
- Impact of chromatin structure on sequence variability in the human genome.Nature structural & molecular biology · 2011Article
- Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Comparative analyses of single-nucleotide polymorphisms in the TNF promoter region provide further validation for the vervet monkey model of obesity.Comparative medicine · 2009Article
- Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.Science (New York, N.Y.) · 2009Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral millions single nucleotide polymorphisms (SNPs) have already been collected and deposited in public databases and these are important resources not only for use as markers to identify disease-associated genes, but also to understand the mechanisms that underlie the genome diversification.
resultsA spectrum analysis of SNP density distribution in the genomic regions around transcription start sites (TSSs) revealed a remarkable periodicity of 146 nucleotides. This periodicity was observed in the regions that were associated with CpG islands (CGIs), but not in the regions without CpG islands (nonCGIs). An analysis of the sequence divergence of the same genomic regions between humans and chimpanzees also revealed a similar periodical pattern in CGI. The occurrences of any mono- or di-nucleotide sequences in these regions did not reveal such a periodicity, thus indicating that an interpretation of this periodicity solely based on the sequence-dependent susceptibility to mutation is highly unlikely.
conclusionThe periodical patterns of nucleotide variability suggest the location of nucleosomes that are phased at TSS, and can be viewed as the genetic footprint of the chromatin state that has been maintained throughout mammalian evolutionary history. The results suggest the possible involvement of the nucleosome structure in the promoter function, and also a fundamental functional/structural difference between the two promoter classes, i.e., those with and without CGIs.
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